full_algorithm_helpers.py

#!/pkg/python/3.7.4/bin/python3
from seeding_algorithm_core import *
from node_pair_extraction_helpers import *
from index_helpers import *
from odv_helpers import *
from ortholog_helpers import *
from patch_helpers import *
from graph_helpers import *

def get_gtag_run_info(gtag1, gtag2, g1_alph=True, g2_alph=True, algo='stairs', lDEG=2):
    g1_index_path = get_index_path(gtag1, alph=g1_alph, algo=algo, lDEG=lDEG)
    g2_index_path = get_index_path(gtag2, alph=g2_alph, algo=algo, lDEG=lDEG)
    g1_graph_path = get_graph_path(gtag1)
    g2_graph_path = get_graph_path(gtag2)
    g1_to_g2_orthologs = get_g1_to_g2_orthologs(gtag1, gtag2)
    return (g1_index_path, g1_graph_path, g2_index_path, g2_graph_path, g1_to_g2_orthologs)

def get_alphrev_gtag_run_infos(gtag1, gtag2, algo='stairs'):
    infos = []
    
    for g1_alph in [True, False]:
        for g2_alph in [True, False]:
            infos.append(get_gtag_run_info(gtag1, gtag2, g1_alph=g1_alph, g2_alph=g2_alph), algo=algo)

    return infos

def get_alphrev_strs():
    strs = []
    
    for g1_alph in [True, False]:
        for g2_alph in [True, False]:
            str_tup = ('alph' if g1_alph else 'rev', 'alph' if g2_alph else 'rev')
            strs.append(''.join(str_tup))

    return strs

def investigate_alphrev_effect(gtag1, gtag2):
    for alphrev_str, run_info in zip(get_alphrev_strs(), get_alphrev_gtag_run_infos(gtag1, gtag2)):
        seeds, seed_metrics, extr_metrics = raw_full_low_param_run(*run_info)
        print(f'{gtag1}-{gtag2} ({alphrev_str}): {len(seeds)} {seed_metrics} {extr_metrics}')

# low param means T=0, M=1, p=0, o=0 with only two index files (no combining)
def raw_full_low_param_run(s1_index_path, s1_graph_path, s2_index_path, s2_graph_path, s1_to_s2_orthologs, prox=1, target_num_matching=1, k=8):
    s1_index = get_patched_index(k, s1_index_path, s1_graph_path, prox=prox, target_num_matching=target_num_matching)
    s2_index = get_patched_index(k, s2_index_path, s2_graph_path, prox=prox, target_num_matching=target_num_matching)
    seeds = find_seeds(s1_index, s2_index, SeedingAlgorithmSettings(max_indices=1, sims_threshold=0), print_progress=False)
    return seeds

def get_all_metrics(seeds, g1_to_g2_ort, gtag1='', gtag2=''):
    from analysis_helpers import get_avg_size, get_seed_nc

    avg_size = get_avg_size(seeds)
    seed_nc = get_seed_nc(seeds, g1_to_g2_ort)
    seed_metrics = (avg_size, seed_nc)

    all_node_pairs = extract_node_pairs(seeds, ignore_deg_1=True, gtag1=gtag1, gtag2=gtag2)
    extr_vol = len(all_node_pairs)
    extr_nc = len(get_orthopairs_list(all_node_pairs, g1_to_g2_ort))
    extr_metrics = (extr_vol, extr_nc)

    return (seed_metrics, extr_metrics)

def seeds_to_str(seeds):
    lines = []
    
    for gid, entry1, entry2 in seeds:
        lines.append(f'{gid}\t{",".join(entry1)}\t{",".join(entry2)}')

    return '\n'.join(lines) + '\n'

# does everything. period.
def simplified_run_with_metrics(gtag1, gtag2, algo='stairs', prox=1, target_num_matching=1, overwrite=False, silent=False):
    from file_helpers import file_exists
    from ortholog_helpers import get_g1_to_g2_orthologs

    seeds_path = get_seeds_path(gtag1, gtag2, algo=algo, prox=prox, target_num_matching=target_num_matching)

    if overwrite or not file_exists(seeds_path):
        seeds = raw_full_low_param_run(*get_gtag_run_info(gtag1, gtag2, algo=algo), prox=prox, target_num_matching=target_num_matching)
        seeds_str = seeds_to_str(seeds)
        write_to_file(seeds_str, seeds_path)
    else:
        if not silent:
            print(f'using old seeds file for {gtag1}-{gtag2}', file=sys.stderr)

        seeds = read_in_seeds(seeds_path)

    g1_to_g2_ort = get_g1_to_g2_orthologs(gtag1, gtag2)
    seed_metrics, extr_metrics = get_all_metrics(seeds, g1_to_g2_ort, gtag1=gtag1, gtag2=gtag2)
    return (seeds, seed_metrics, extr_metrics)

if __name__ == '__main__':
    from full_report_helpers import gen_all_indexes

    gtag1 = sys.argv[1]
    gtag2 = sys.argv[2]
    seeds, seed_metrics, extr_metrics = simplified_run_with_metrics(gtag1, gtag2)
    print(len(seeds), seed_metrics, extr_metrics)